Can I Cycles bake all diffuse lighting in one go?
We are facing a similar problem and I am currently investigating the same issue. In our automated lightmap process we use the following workaround to get the indirect and direct light information without having to bake two passes (we still bake 2 passes but one takes a split second).

Maybe this could be a solution for you:


Bake a combined map with x samples
Bake a color map with 1 sample (that is enough to get the full information)
subtract the color map from the combined map (via node setup or photoshop)
problems: if your textures/materials are too dark, you loose information due to the subtraction and overexposed black pixels


I am planning to make a feature request to combine the passes, since it takes significally longer to bake two passes rather then baking a combined pass. Maybe you would like to be a part of it?